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Updated: Jul 2, 2026
Gel-seq: A Method for Simultaneous Sequencing Library Preparation of DNA and RNA Using Hydrogel Matrices
Published on: March 26, 2018
GLASS-seq: a gel-anchored, ligation-assisted, scalable biosensing platform for low-cost regional spatial
Liu Chen1, Xucong Teng1, Ai-Hui Tang2
1Anhui Province Key Laboratory of Biomedical Imaging and Intelligent Processing, Hefei Comprehensive National Science Center Institute of Artificial Intelligence, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei, Anhui, China.
GLASS-seq is a new spatial transcriptomics method using probe ligation and hydrogel anchoring for cost-effective RNA quantification. This scalable technique offers high fidelity and reproducibility without specialized equipment, enabling regional gene expression analysis.
Area of Science:
- Molecular Biology
- Genomics
- Biotechnology
Background:
- Spatial transcriptomics methods face limitations in cost, equipment requirements, and detection sensitivity for low-abundance targets in small regions.
- Existing techniques often require specialized instrumentation, hindering broader accessibility.
Purpose of the Study:
- To develop a cost-effective, scalable, and accessible spatial transcriptomics platform.
- To enable digital sequencing readouts of in situ RNA recognition with high fidelity and reproducibility.
Main Methods:
- GLASS-seq (Gel-anchored, Ligation-Assisted, Scalable Spatial sequencing) utilizes a hydrogel-embedded, probe-ligation biosensing approach.
- Target-specific split probes are joined by SplintR ligase upon dual recognition, with ligation products immobilized in a polyacrylamide network.
- Minimal PCR appends spatial barcodes for ROI-indexed library generation, compatible with immunofluorescence and in situ hybridization.
Main Results:
- GLASS-seq demonstrated high capture fidelity (>96%), robust read retention (≈81%), and strong reproducibility (r ≥ 0.98).
- Analysis of mouse brain sections with a 731-gene panel in 212 ROIs showed alignment with neuroanatomy and public ISH atlases (r = 0.85).
- The method achieved a low cost per section (∼$512) and modest sequencing depth (∼0.42 Gb per ROI).
Conclusions:
- GLASS-seq provides a robust, economical, and scalable solution for regional spatial RNA quantification.
- The platform overcomes limitations of existing methods, making spatial transcriptomics more accessible for large cohorts and translational research.
- It enables precise regional gene expression profiling across various tissues without specialized instrumentation.
